Re: "GroupPressure no" resulting in negative pressure outputs

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Fri Nov 26 2010 - 13:03:56 CST

Dear Jerome,

> It does sound like a problem. To distinguish whether it comes from
> pressure measurement itself or from the barostat, it would be very
> useful to repeat this comparative test in constant volume simulations.

To achieve running an NVT ensemble simulation, I did the following:
- switch off the "LangevinPiston" options
- useFlexibleCell "yes"->"no"

I have four runs of the same system:
a) with piston (NPT), group pressure yes
b) with piston (NPT), group pressure no
c) NVT, group pressure yes
d) NVT, group pressure no

with the following mean GPRESSAVG values:

a) (1.1+-1.6)bar
b) (-14.1+-2.6)bar
c) (8.8+-12.8)bar
d) (-0.94+-13.01)bar

means are over >=0.5ns trajectories. Uncertainties are simple standard
deviations (energy fluctuations are numerically too large to compute
Boltzmann averages).

My Questions:
1.)
Does this help at all? If yes, please explain: are you simply looking
for differences in the GPRESSAVG output?
Or are there distinct pressure values/differences in the NVT that I
would have to expect physically?
2.)
As a consequence, is it safer to use GroupPressure, even if the
"rigidBonds" option is not used?

Cheers,
Sebastian

PS:
Qu'est-ce que c'est, je ne trouve pas "Fête de la récolte" en wikipedia
pour la France!
;-)

On 11/25/10 3:56 PM, Jérôme Hénin wrote:
> Hi Sebastian,
>
> On 25 November 2010 20:51, Sebastian Stolzenberg
> <s.stolzenberg_at_gmail.com> wrote:
>> Happy Thanksgiving, All,
> Not everyone on this list celebrates Thanksgiving, but thank you all
> the same :-)
>
>
>> "useGroupPressure no" is a default option and not required, when not using
>> "rigidBonds".
>>
>> For the following, I measure "pressure" from the log files using the NAMD
>> Plot plugin by observing "PRESSAVG" or "GPRESSAVG".
>>
>> For a system with box size>100x100x90A^3 and no rigidBonds (FlexibleCell
>> yes):
>> Using "useGroupPressure yes",
>> I get pressures of about 1+-2bar
>> and with "useGroupPressure no",
>> I get pressures of about -13+-3bar
>>
>> Fluctuations are larger for "useGroupPressure no" vs. ""useGroupPressure
>> yes", but within these fluctuations, the "useGroupPressure no" doesn't seem
>> to give me the correct pressure that I set via:
>>
>> ..
>> LangevinPiston on
>> LangevinPistonTarget 1.01325
>> LangevinPistonPeriod 200
>> LangevinPistonDecay 50
>> LangevinPistonTemp 310
>> ..
>> PME yes
>> PMEGridSpacing 1.0
>> ..
>>
>> Talking to colleagues of mine, they appear to have exactly the same issue
>> for different systems.
> It does sound like a problem. To distinguish whether it comes from
> pressure measurement itself or from the barostat, it would be very
> useful to repeat this comparative test in constant volume simulations.
>
> Best,
> Jerome

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